Organic optoelectronic nanostructures are essential in future large‐area nanoscale electronic circuits but their morphology, structure, and performance currently remain difficult to control. Here a new, simple, general anode aluminium oxide (AAO)‐template assisted electrochemical deposition method is developed for the preparation of uniform single‐crystalline small molecule nanowires in large quantities. Using rubrene as prototype, selected‐area electron diffraction and X‐ray diffraction results reveal that the obtained individual nanowires are single crystalline, while both of orthorhombic and triclinic rubrene nanowires are present. With red and yellow emissions at maximum wavelengths of 570 and 558 nm, respectively, the orthorhombic and triclinic nanowires show a 10× difference on field‐effect transistor hole mobility, in good agreement with theoretical calculation observations. Unexpectedly, the visible‐light photoresponse of the two kinds of nanowires does not show significant difference, suggesting a better charge separation and carrier photogeneration in triclinic nanowires. Overall, this is the first report on the structure–property correlations between triclinic and orthorhombic rubrene single crystalline nanowires, and the methodology launched here is applicable to different molecular semiconductors and hybrid nanostructures for next‐generation integrated optoelectronics.